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Protein

Formamidopyrimidine-DNA glycosylase

Gene

mutM

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.UniRule annotation

Catalytic activityi

Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine.UniRule annotation
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.UniRule annotation

Cofactori

Zn2+UniRule annotationNote: Binds 1 zinc ion per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei2 – 21Schiff-base intermediate with DNAUniRule annotation
Active sitei3 – 31Proton donorUniRule annotation
Active sitei57 – 571Proton donor; for beta-elimination activityUniRule annotation
Binding sitei90 – 901DNAUniRule annotation
Binding sitei109 – 1091DNAUniRule annotation
Binding sitei150 – 1501DNAUniRule annotation
Active sitei259 – 2591Proton donor; for delta-elimination activityUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri235 – 26935FPG-typeUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. damaged DNA binding Source: InterPro
  2. oxidized purine nucleobase lesion DNA N-glycosylase activity Source: UniProtKB-HAMAP
  3. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. base-excision repair Source: InterPro
  2. nucleotide-excision repair Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase, Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-200-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Formamidopyrimidine-DNA glycosylaseUniRule annotation (EC:3.2.2.23UniRule annotation)
Short name:
Fapy-DNA glycosylaseUniRule annotation
Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyase MutMUniRule annotation (EC:4.2.99.18UniRule annotation)
Short name:
AP lyase MutMUniRule annotation
Gene namesi
Name:mutMUniRule annotation
Synonyms:fpgUniRule annotation
Ordered Locus Names:VP0189
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002493 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 269268Formamidopyrimidine-DNA glycosylasePRO_0000170883Add
BLAST

Interactioni

Subunit structurei

Monomer.UniRule annotation

Protein-protein interaction databases

STRINGi223926.VP0189.

Structurei

3D structure databases

ProteinModelPortaliQ87T81.
SMRiQ87T81. Positions 2-269.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the FPG family.UniRule annotation
Contains 1 FPG-type zinc finger.UniRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri235 – 26935FPG-typeUniRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0266.
HOGENOMiHOG000020881.
KOiK10563.
OMAiKYSKFFA.
OrthoDBiEOG6QP131.

Family and domain databases

HAMAPiMF_00103. Fapy_DNA_glycosyl.
InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR012319. DNA_glycosylase/AP_lyase_cat.
IPR020629. Formamido-pyr_DNA_Glyclase.
IPR010979. Ribosomal_S13-like_H2TH.
IPR000214. Znf_DNA_glyclase/AP_lyase.
IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
[Graphical view]
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view]
SMARTiSM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view]
SUPFAMiSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
TIGRFAMsiTIGR00577. fpg. 1 hit.
PROSITEiPS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q87T81-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPELPEVEVS RMGISPHMVG QTIKAFVFRT PKLRWDIPQE LKLLEGQVIR
60 70 80 90 100
NIRRRAKYLL IDTDQGTAIV HLGMSGSLRV LDADFPAAKH DHVDLKLTNG
110 120 130 140 150
KVLRYNDPRR FGAWLWCAPG ESHAVLEHMG PEPLTDAFNS EYIADKAQGK
160 170 180 190 200
RVAVKQFIMD NKVVVGVGNI YANESLFKSR ILPTRQAGQV TPQEWVLLVE
210 220 230 240 250
NIKATLKIAI NQGGTTLKDF AQADGKPGYF AQELLVYGKA GEPCPECGEP
260
LQELKIGQRN TFFCNECQQ
Length:269
Mass (Da):30,096
Last modified:January 23, 2007 - v3
Checksum:i77A1CB9CEF07E8C6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC58452.1.
RefSeqiNP_796568.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC58452; BAC58452; BAC58452.
GeneIDi1187656.
KEGGivpa:VP0189.
PATRICi20138612. VBIVibPar50997_0181.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC58452.1.
RefSeqiNP_796568.1. NC_004603.1.

3D structure databases

ProteinModelPortaliQ87T81.
SMRiQ87T81. Positions 2-269.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VP0189.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC58452; BAC58452; BAC58452.
GeneIDi1187656.
KEGGivpa:VP0189.
PATRICi20138612. VBIVibPar50997_0181.

Phylogenomic databases

eggNOGiCOG0266.
HOGENOMiHOG000020881.
KOiK10563.
OMAiKYSKFFA.
OrthoDBiEOG6QP131.

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-200-MONOMER.

Family and domain databases

HAMAPiMF_00103. Fapy_DNA_glycosyl.
InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
IPR012319. DNA_glycosylase/AP_lyase_cat.
IPR020629. Formamido-pyr_DNA_Glyclase.
IPR010979. Ribosomal_S13-like_H2TH.
IPR000214. Znf_DNA_glyclase/AP_lyase.
IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
[Graphical view]
PfamiPF01149. Fapy_DNA_glyco. 1 hit.
PF06831. H2TH. 1 hit.
PF06827. zf-FPG_IleRS. 1 hit.
[Graphical view]
SMARTiSM00898. Fapy_DNA_glyco. 1 hit.
[Graphical view]
SUPFAMiSSF46946. SSF46946. 1 hit.
SSF81624. SSF81624. 1 hit.
TIGRFAMsiTIGR00577. fpg. 1 hit.
PROSITEiPS51068. FPG_CAT. 1 hit.
PS01242. ZF_FPG_1. 1 hit.
PS51066. ZF_FPG_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae."
    Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.
    Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry nameiFPG_VIBPA
AccessioniPrimary (citable) accession number: Q87T81
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 23, 2003
Last sequence update: January 23, 2007
Last modified: April 29, 2015
This is version 88 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.